LAMMPS (8 Jul 2015)
units real
boundary p p p

atom_style full
bond_style harmonic
angle_style harmonic
special_bonds lj/coul 0.0 0.0 0.5

pair_style lj/cut/coul/long 12.0 12.0
kspace_style pppm 1.0e-3

comm_modify vel yes
read_data data.swm4-ndp
  orthogonal box = (-12 -12 -12) to (12 12 12)
  1 by 2 by 2 MPI processor grid
  reading atoms ...
  2500 atoms
  scanning bonds ...
  1 = max bonds/atom
  scanning angles ...
  1 = max angles/atom
  reading bonds ...
  2000 bonds
  reading angles ...
  500 angles
  4 = max # of 1-2 neighbors
  3 = max # of 1-3 neighbors
  3 = max # of 1-4 neighbors
  4 = max # of special neighbors

pair_coeff    1    1      0.210939     3.183950  # ODw ODw
pair_coeff    *   2*      0.000000     0.0

group ATOMS type 1:3
2000 atoms in group ATOMS
group CORES type 1
500 atoms in group CORES
group DRUDES type 4
500 atoms in group DRUDES

variable TK equal 300.0
variable TDK equal 1.0
variable PBAR equal 1.0

neighbor 2.0 bin

timestep 1.0

fix DRUDE all drude C N N D

velocity ATOMS create ${TK} 12345
velocity ATOMS create 300 12345
velocity DRUDES create ${TDK} 12345
velocity DRUDES create 1 12345

delete_bonds ATOMS multi
PPPM initialization ...
  G vector (1/distance) = 0.217457
  grid = 10 10 10
  stencil order = 5
  estimated absolute RMS force accuracy = 0.197288
  estimated relative force accuracy = 0.000594128
  using double precision FFTs
  3d grid and FFT values/proc = 1500 300
Rebuild special list taking Drude particles into account
Old max number of 1-2 to 1-4 neighbors: 4
New max number of 1-2 to 1-4 neighbors: 4 (+0)
Neighbor list info ...
  1 neighbor list requests
  update every 1 steps, delay 10 steps, check yes
  master list distance cutoff = 14
  2000 total bonds, 500 turned on, 1500 turned off
  500 total angles, 0 turned on, 500 turned off
  0 total dihedrals, 0 turned on, 0 turned off
  0 total impropers, 0 turned on, 0 turned off

fix TEMP all langevin/drude ${TK} 100. 1256 ${TDK} 20. 13977 zero yes
fix TEMP all langevin/drude 300 100. 1256 ${TDK} 20. 13977 zero yes
fix TEMP all langevin/drude 300 100. 1256 1 20. 13977 zero yes
fix NPH ATOMS rigid/nph/small molecule iso ${PBAR} ${PBAR} 500.
fix NPH ATOMS rigid/nph/small molecule iso 1 ${PBAR} 500.
fix NPH ATOMS rigid/nph/small molecule iso 1 1 500.
500 rigid bodies with 2000 atoms
  0.832099 = max distance from body owner to body atom
fix NVE DRUDES nve

compute TEMP all temp/drude

thermo_style custom step cpu etotal ke pe ebond eangle evdwl ecoul elong press vol temp c_TEMP[1] c_TEMP[2]
thermo 20

run 2000
PPPM initialization ...
  G vector (1/distance) = 0.217457
  grid = 10 10 10
  stencil order = 5
  estimated absolute RMS force accuracy = 0.197288
  estimated relative force accuracy = 0.000594128
  using double precision FFTs
  3d grid and FFT values/proc = 1500 300
Rebuild special list taking Drude particles into account
Old max number of 1-2 to 1-4 neighbors: 4
New max number of 1-2 to 1-4 neighbors: 4 (+0)
Memory usage per processor = 15.0906 Mbytes
Step CPU TotEng KinEng PotEng E_bond E_angle E_vdwl E_coul E_long Press Volume Temp TEMP[1] TEMP[2] 
       0            0    4568.0415    903.41148      3664.63    623.46454            0    2890.2449    157955.66   -157804.74    244591.08        13824    202.18534    295.64644    14.858785 
      20   0.47649789    2915.1578    4579.5774   -1664.4195    561.91893            0    600.76451    155095.13   -157922.23     27379.77    14058.574    1024.9188    1455.9194    160.86778 
      40   0.97488093    1320.1721    3337.6372   -2017.4651    726.83344            0     585.5439    154587.28   -157917.12    18749.425    14485.651    746.97006    1101.4061    36.530914 
      60    1.4631288    284.06852    2671.4325   -2387.3639    575.54157            0     387.8792    154580.74   -157931.53    12104.741    15031.425    597.87207    886.98502    18.450413 
      80     1.937151   -462.53017     2214.284   -2676.8142    560.36347            0    254.65245    154447.22   -157939.05    6285.2465    15651.216    495.56131    739.13811    7.4024411 
     100    2.3922298   -965.19662     1839.831   -2805.0276    544.59528            0    115.80812    154469.59   -157935.02    2361.9397     16295.72    411.75795    615.12769     4.196977 
     120     2.832803   -1316.6351     1649.585   -2966.2202     554.6664            0    50.928925    154365.49    -157937.3   -493.85523    16925.293    369.18052     552.0345    2.7331855 
     140    3.2340388   -1590.9162    1440.6669   -3031.5831    526.07679            0    -24.44055    154404.35   -157937.57   -2586.2431    17517.285    322.42421    482.16117     2.297578 
     160    3.6521859   -1742.3401    1326.8812   -3069.2213    539.49044            0   -43.846659     154369.1   -157933.96   -3549.2196    18059.707    296.95874    444.11026    2.0644677 
     180     4.033325   -1895.1332    1224.1816   -3119.3148    555.27887            0   -18.261233    154275.94   -157932.27   -3762.2304    18545.518    273.97437    409.78413     1.806893 
     200    4.4333398   -2004.4682    1176.8828    -3181.351     565.0443            0   0.21425471    154190.38   -157936.99   -4346.6036    18973.342    263.38879    393.94856    1.7400558 
     220    4.8055639   -2094.1888    1098.3856   -3192.5744    592.45764            0     36.50238    154113.36   -157934.89   -4135.0794    19341.735    245.82095    367.67707     1.617053 
     240    5.1688328   -2178.9829    1086.8322   -3265.8151    617.63697            0    96.836936    153957.27   -157937.56   -4121.5262      19651.8    243.23528    363.77401    1.6722646 
     260    5.5313618   -2264.8265    1078.4348   -3343.2613    663.35817            0    167.76882    153763.13   -157937.52   -3799.3346    19907.052    241.35592    360.97385    1.6377289 
     280    5.8937738   -2325.7764    1097.4356    -3423.212    717.74089            0     235.0127    153562.96   -157938.92   -3696.0526    20111.414    245.60833    367.31076    1.7042318 
     300     6.254128   -2390.4932    1068.1054   -3458.5986    751.64681            0    295.31516    153435.34    -157940.9   -3512.2095    20268.754    239.04419    357.49427     1.665921 
     320    6.6138928   -2455.1776    1041.7419   -3496.9195     765.8972            0    331.14997       153345   -157938.97   -3020.0674    20383.474    233.14397    348.62385    1.7179273 
     340    6.9748628   -2536.9935    1050.7304   -3587.7239    793.64536            0    352.69908    153205.74   -157939.81   -3447.9127    20457.612    235.15562     351.6381    1.7214573 
     360    7.3319299   -2603.5606    966.90943     -3570.47    819.14306            0    391.00909    153158.89   -157939.51    -3164.629    20490.764    216.39631    323.51872    1.7254892 
     380     7.691319    -2594.787    1024.7927   -3619.5797    836.44816            0    434.32118    153047.12   -157937.47   -2902.9345    20485.923    229.35071    342.91482    1.7641915 
     400     8.044276   -2647.3896    982.46478   -3629.8543    864.59805            0    479.08516     152963.5   -157937.04   -2535.9236    20447.668    219.87764    328.69587    1.8030508 
     420    8.3971269   -2687.5263    1023.0437     -3710.57    928.04551            0    538.49845    152760.83   -157937.94   -2383.6292    20380.427    228.95928    342.31215    1.8044964 
     440     8.753284   -2765.2192    999.28342   -3764.5026    966.26754            0    577.15359    152631.24   -157939.17   -2391.0923    20286.676    223.64168    334.34309    1.7947669 
     460    9.1102748   -2806.7385    1004.2311   -3810.9696    996.86893            0    599.41867    152532.79   -157940.05   -2476.5754    20168.782    224.74899    335.97767    1.8475589 
     480     9.471664   -2830.2582    1013.6925   -3843.9506    1009.5553            0    624.64584    152464.58   -157942.73   -2210.7254    20027.747    226.86645    339.14841    1.8588685 
     500    9.8365009   -2865.4993     1024.473   -3889.9723    1017.2606            0    658.56598    152375.13   -157940.93   -2047.5735    19865.992    229.27916    342.78576    1.8103481 
     520    10.207523   -2918.9299    973.10292   -3892.0328     1049.357            0    699.16951    152300.27   -157940.83   -1453.4121    19688.211    217.78243    325.51403    1.8799495 
     540    10.583098   -2970.1121    925.84385    -3895.956    1077.9578            0    758.25478    152208.67   -157940.84   -821.19447    19499.417    207.20575    309.67486    1.8442683 
     560    10.962813   -3008.9942    954.33133   -3963.3255    1114.7309            0    751.85274    152112.75   -157942.66   -1023.0801    19304.314    213.58131    319.23167    1.8463043 
     580    11.351938   -3069.9822    951.38041   -4021.3626    1127.8186            0    765.20411    152027.82    -157942.2   -954.30565    19101.694    212.92089    318.20155    1.9391088 
     600     11.74351   -3090.3867    973.25557   -4063.6423    1123.3487            0    744.86978    152009.46   -157941.32   -1226.2333    18891.444    217.81659     325.5949    1.8227604 
     620    12.138507   -3114.2347    1002.2136   -4116.4483    1159.4812            0    766.24573    151899.05   -157941.23   -1406.6638    18672.922    224.29746    335.32178    1.8002314 
     640     12.53874   -3160.3172    973.01388   -4133.3311    1181.5814            0    805.79135    151821.94   -157942.65   -1444.0821    18448.163     217.7625    325.51017    1.8464735 
     660    12.945363   -3185.1871    975.57462   -4160.7618    1177.1798            0    795.84414    151809.59   -157943.38   -962.08053    18220.064     218.3356    326.36793    1.8252243 
     680    13.358243   -3226.8034    977.21534   -4204.0187    1215.3088            0     862.3869    151662.05   -157943.76   -538.09214    17991.009     218.7028    326.90984    1.8513045 
     700    13.774714   -3267.0358    979.72611   -4246.7619    1229.2873            0    878.80049    151588.58   -157943.43    -526.4724    17765.058    219.26471    327.74412      1.86738 
     720    14.198356   -3275.0063    987.91851   -4262.9248    1260.2342            0    905.19546    151515.01   -157943.36   -285.51035    17544.004    221.09819    330.48021    1.8901628 
     740    14.624448   -3298.9204      992.679   -4291.5994    1283.7665            0    917.78414    151449.24   -157942.39    351.98558    17329.448     222.1636    332.09658     1.843264 
     760     15.05056   -3316.7113    1010.6458   -4327.3571    1296.6728            0     951.2091    151368.47   -157943.71    419.51796    17123.095    226.18459    338.07068    1.9518407 
     780    15.504961   -3294.5707    1053.9493     -4348.52     1300.722            0    975.60682    151317.15      -157942    1040.7668    16927.715    235.87602    352.49204    2.1793007 
     800    15.933704   -3363.0539    987.22337   -4350.2773    1325.1641            0     1013.664    151255.26   -157944.36    1462.6199      16747.7    220.94262    330.24432    1.8985721 
     820    16.364414   -3437.2117     980.5397   -4417.7514    1350.8684            0     1029.953    151144.46   -157943.03    817.95684    16584.026     219.4468     327.9943    1.9129039 
     840    16.799625   -3465.5868    981.23685   -4446.8236    1388.7125            0    1043.4314    151066.43    -157945.4    1366.0731    16434.707    219.60282    328.17006    2.0308095 
     860    17.241996   -3460.2301    1020.3681   -4480.5981    1418.4709            0    1090.9207    150954.21    -157944.2    1450.0443    16300.524    228.36046    341.31823    2.0218282 
     880    17.688347   -3499.5491    994.43799   -4493.9871    1444.4283            0     1113.276    150893.43   -157945.12    2227.6739    16183.439    222.55726    332.59403    2.0408296 
     900    18.136371   -3526.9176    952.87144    -4479.789    1443.8422            0    1118.5107    150902.72   -157944.87    2220.1643    16085.505    213.25458    318.69359    1.9574553 
     920    18.599828   -3545.2479    976.95271   -4522.2006    1443.4309            0    1118.3924    150859.69   -157943.71    2107.6215    16006.466    218.64402    326.75181    1.9926282 
     940    19.064528   -3560.4406    994.62379   -4555.0644    1431.3624            0    1098.4902    150860.38    -157945.3    1495.9356     15944.46    222.59885    332.62316    2.0953461 
     960    19.529192    -3590.569    964.78915   -4555.3582    1431.9284            0    1092.1793    150866.87   -157946.34    1559.1687    15897.003    215.92179     322.6406    2.0442546 
     980    19.991661   -3599.6592    986.56344   -4586.2227    1435.7543            0    1034.8682    150889.35    -157946.2    679.01087    15862.242    220.79492    330.01359    1.9307016 
    1000    20.427668   -3634.9266    939.78172   -4574.7083    1424.4834            0     1022.664    150924.73   -157946.59    733.04572    15834.345    210.32508    314.30018    1.9584145 
    1020    20.873712    -3669.298    934.76265   -4604.0606       1452.3            0    1016.3445    150873.46   -157946.16    143.60284    15811.749     209.2018    312.55492    2.0808526 
    1040    21.319204   -3682.4175    935.86127   -4618.2788    1447.0344            0    1035.4526    150844.58   -157945.34    515.93558    15792.261    209.44767    312.98247    1.9790896 
    1060    21.766855   -3704.0833    901.03929   -4605.1226    1476.4857            0     1067.779    150794.42    -157943.8    1092.0636    15777.267    201.65444     301.3325    1.8948719 
    1080    22.214459   -3699.4923    921.66268    -4621.155    1475.7351            0    1079.7576     150767.2   -157943.85    1003.4205    15769.569       206.27    308.27973    1.8458618 
    1100    22.662445   -3667.6761    957.47147   -4625.1476    1507.2355            0    1102.9252    150708.15   -157943.46    927.20789    15768.898    214.28408    320.17339    2.0742837 
    1120    23.085055   -3668.1399    935.38917   -4603.5291    1507.3367            0    1080.9826     150753.9   -157945.75    810.87137    15775.175    209.34202    312.79082    2.0279075 
    1140    23.534417   -3710.7149    937.22068   -4647.9356    1499.5413            0    1020.4759    150776.54   -157944.49   -138.27816    15786.277    209.75191    313.34734    2.1346658 
    1160    23.985544   -3711.7493    900.74897   -4612.4983    1430.3269            0    990.84122    150911.11   -157944.78    8.4592568    15798.538    201.58947    301.24561    1.8661211 
    1180    24.439474   -3729.7115    928.82825   -4658.5398    1435.7711            0    937.43508    150913.97   -157945.72   -905.33202    15809.125    207.87367    310.65722    1.8872897 
    1200    24.895124   -3738.2838    909.79315    -4648.077    1436.4199            0    938.10918     150922.8   -157945.41   -1112.9968    15812.511    203.61357    304.28121    1.8714711 
    1220    25.352201   -3757.8302    907.08742   -4664.9176    1424.1514            0    930.13653    150924.86   -157944.06   -1078.0621    15807.893    203.00803    303.40134    1.8521625 
    1240    25.780748   -3778.5355    905.88168   -4684.4171    1453.9568            0    959.37689    150846.21   -157943.96   -975.25032    15795.393    202.73818    303.00695     1.778808 
    1260    26.238145   -3773.7584    879.94641   -4653.7048    1473.5812            0      1002.67    150815.41   -157945.36   -360.58922    15776.466    196.93381     294.2433    1.9174557 
    1280    26.696751   -3755.4956    904.13603   -4659.6316    1493.7103            0    1017.8327    150773.94   -157945.12   -256.88128    15755.525     202.3475    302.35592    1.9294965 
    1300    27.158244   -3754.9246    903.51795   -4658.4425    1498.1329            0    1006.1786    150782.15    -157944.9    -455.2258    15732.436    202.20917    302.19365    1.8353806 
    1320    27.619539   -3758.1232    913.25769   -4671.3808    1500.2049            0    1032.0703    150739.71   -157943.37   -251.62277    15706.775    204.38895    305.38485    1.9968111 
    1340    28.079132   -3784.7481    937.61449   -4722.3626    1505.7439            0    993.46365    150723.27   -157944.84    -853.9871     15680.38    209.84005    313.60153    1.8911101 
    1360    28.514251   -3808.7787    864.89279   -4673.6715    1475.0618            0    1009.2569    150785.65   -157943.64   -331.64382    15650.208    193.56478    289.20988    1.8929896 
    1380    28.975972   -3798.7281     892.2622   -4690.9903     1465.561            0    993.58051    150793.83   -157943.96   -567.64508    15617.156    199.69011    298.39786    1.8757635 
    1400    29.439238   -3807.9228    893.51775   -4701.4406    1459.3875            0    1000.4434    150784.38   -157945.65   -456.80001    15580.856    199.97111    298.79789     1.925086 
    1420    29.904427   -3818.6783    890.66153   -4709.3398    1515.8208            0    1064.6851    150655.36   -157945.21    450.86768     15542.76    199.33188    297.83132     1.927452 
    1440    30.368352    -3822.016    910.79285   -4732.8089    1539.2325            0    1076.0339    150597.99   -157946.07    429.02044    15506.302    203.83731    304.53724    2.0216852 
    1460    30.835555   -3821.2117    931.47963   -4752.6914    1540.1582            0    1089.9477    150561.76   -157944.55    645.54716     15472.89    208.46705    311.56653    1.8487206 
    1480    31.306455    -3838.255    920.25737   -4758.5124    1546.6509            0    1107.4468    150533.86   -157946.47    556.76352    15443.298    205.95549    307.74395    1.9637305 
    1500    31.747528   -3839.4323    942.18813   -4781.6204    1557.1836            0    1105.7209    150502.68   -157947.21    535.34633    15417.723    210.86364    315.07463    2.0384198 
    1520    32.218974    -3827.551    925.42642   -4752.9774    1555.4578            0     1097.174    150540.89    -157946.5    680.16246        15396    207.11233    309.42351    2.0793499 
    1540    32.691924   -3836.1802    885.40721   -4721.5874    1558.3851            0    1144.6478    150521.13   -157945.75    1216.5367    15378.972    198.15595    296.02524     2.015983 
    1560    33.164075   -3830.4342    955.31807   -4785.7523    1574.0464            0    1105.7294    150481.06   -157946.59    169.17645    15369.126    213.80214     319.4694    2.0400237 
    1580    33.636497   -3808.4082    948.31996   -4756.7281    1556.8058            0    1079.1205     150552.4   -157945.06    603.87966    15363.124    212.23595    317.13706    2.0112224 
    1600    34.111529   -3835.9681    925.63461   -4761.6027    1575.0508            0    1091.3896    150517.16    -157945.2    356.94873    15359.871    207.15893    309.60148    1.8514712 
    1620    34.558112   -3865.8357    866.45292   -4732.2886    1577.3357            0    1137.1716    150497.63   -157944.43    945.81112    15359.844    193.91394    289.72922    1.8926829 
    1640    35.029171   -3849.5025    884.49282   -4733.9954    1547.0606            0    1101.4292    150561.92   -157944.41    703.96326    15365.598    197.95131    295.76038     1.913597 
    1660    35.495665   -3861.3162    906.62112   -4767.9373    1547.2773            0    1074.8986    150555.48    -157945.6    46.512723    15375.298    202.90367     303.1667    1.9573677 
    1680    35.959871   -3857.7679     907.8657   -4765.6336    1547.7327            0    1089.3299    150543.52   -157946.22    383.48079    15386.165    203.18221     303.5736    2.0202069 
    1700    36.428885   -3869.0902    891.82145   -4760.9117    1512.1728            0    1012.6239    150658.31   -157944.02   -488.95961    15397.869    199.59147    298.24425    1.8990607 
    1720    36.903833   -3870.4685    893.82411   -4764.2926    1485.7646            0    989.27762    150706.25   -157945.59   -542.70653    15406.338    200.03967    298.80302    2.1113341 
    1740    37.380529   -3847.3408    893.93384   -4741.2746    1509.8117            0    1031.6641    150663.04   -157945.79    -307.1162    15410.521    200.06423    298.90093    2.0090208 
    1760    37.827319    -3840.438    868.84851   -4709.2865     1474.404            0     1018.599     150744.2   -157946.49   -276.44721    15412.838    194.45008    290.51398    1.9203414 
    1780    38.297568   -3842.0322    910.50606   -4752.5383    1494.2187            0    1002.3762    150696.05   -157945.18   -585.57252    15412.983    203.77313    304.47127    1.9624414 
    1800     38.76671   -3861.9431    881.98228   -4743.9254    1471.6721            0    978.01808    150752.55   -157946.17   -711.07254    15409.636    197.38944    294.90206    1.9749925 
    1820    39.233968   -3890.8613    856.10452   -4746.9658    1505.1405            0     991.9875    150701.72   -157945.82   -509.17282    15401.428    191.59795    286.24213    1.9311068 
    1840    39.704207   -3860.2881    907.57785    -4767.866    1492.5264            0    999.80677    150685.45   -157945.65   -697.50098    15387.414    203.11779    303.52338    1.9123566 
    1860    40.174673   -3879.0681    938.58496    -4817.653    1532.9628            0    1046.6919    150550.41   -157947.72   -311.83188     15369.15    210.05724    313.84514    2.0580305 
    1880    40.646746   -3871.1182    925.64972   -4796.7679    1531.6363            0    1064.5321    150553.96    -157946.9     136.0161    15350.638    207.16231    309.48972    2.0957912 
    1900    41.120691   -3868.9005     949.1652   -4818.0657    1593.1686            0    1150.4095    150384.01   -157945.65    753.94006    15333.301    212.42512    317.39691    2.0615952 
    1920     41.59464   -3868.6343    954.03473    -4822.669    1610.5603            0    1192.2159    150320.88   -157946.33    1209.5547    15321.106    213.51493    319.06152     2.011006 
    1940    42.037294   -3884.0548    926.13369   -4810.1885    1595.5448            0    1167.6153    150372.25    -157945.6    1289.8018    15318.433    207.27062    309.70304    1.9619634 
    1960    42.507917    -3889.403    953.52537   -4842.9284    1598.8799            0    1116.9498    150388.89   -157947.65    327.93587    15323.804    213.40093     318.9112    1.9579466 
    1980    42.973861   -3911.0951    911.40927   -4822.5043    1553.4244            0    1085.4519    150485.64   -157947.02    169.14591    15332.113    203.97527    304.77814    1.9637281 
    2000     43.43889   -3892.0279    902.31728   -4794.3452    1534.2125            0     1088.703    150530.25   -157947.51    473.37009    15341.654    201.94046    301.71557    1.9929295 
Loop time of 43.4389 on 4 procs for 2000 steps with 2500 atoms

Pair  time (%) = 30.8131 (70.9343)
Bond  time (%) = 0.0167851 (0.0386406)
Kspce time (%) = 2.78529 (6.41196)
Neigh time (%) = 2.7229 (6.26835)
Comm  time (%) = 2.36382 (5.4417)
Outpt time (%) = 0.00704503 (0.0162182)
Other time (%) = 4.72998 (10.8888)

Nlocal:    625 ave 641 max 600 min
Histogram: 1 0 0 0 0 0 0 2 0 1
Nghost:    13465.2 ave 13518 max 13362 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Neighs:    585334 ave 608376 max 546210 min
Histogram: 1 0 0 0 0 0 1 0 1 1

Total # of neighbors = 2341334
Ave neighs/atom = 936.534
Ave special neighs/atom = 4
Neighbor list builds = 100
Dangerous builds = 7

